He became the national leader (Supreme Minister) of the Nation of Islam in 1975 after his father's death. As a result of his personal studies and thinking, he had led the vast majority of the members of the original NOI to mainstream, traditional "Sunni Islam"by 1978. With this merger, he oversaw the largest mass conversion to Islam in the history of the United States. He rejected the previous deification of Wallace Fard Muhammad, accepted whites as fellow-worshippers, forged closer ties with mainstream Muslim communities, and introduced the Five Pillars of Islam into his group's theology.

Splinter groups resisting these changes formed after Elijah Muhammad's death, particularly under Louis Farrakhan, who in 1981 would revive the name Nation of Islam (from Final Call) for his organization. Farrakhan's NOI and previous Final Call claim direct continuity from the pre-1976 NOI.